Class CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector

    • Constructor Detail

      • WgsMetricsWithNonZeroCoverageCollector

        public WgsMetricsWithNonZeroCoverageCollector​(CollectWgsMetricsWithNonZeroCoverage metrics,
                                                      int coverageCap,
                                                      htsjdk.samtools.util.IntervalList intervals)
    • Method Detail

      • addToMetricsFile

        public void addToMetricsFile​(htsjdk.samtools.metrics.MetricsFile<WgsMetrics,​Integer> file,
                                     boolean includeBQHistogram,
                                     CountingFilter dupeFilter,
                                     CountingFilter adapterFilter,
                                     CountingFilter mapqFilter,
                                     CountingPairedFilter pairFilter)
        Description copied from class: AbstractWgsMetricsCollector
        Adds collected metrics and depth histogram to file
        Overrides:
        addToMetricsFile in class AbstractWgsMetricsCollector<htsjdk.samtools.util.SamLocusIterator.RecordAndOffset>
        Parameters:
        file - MetricsFile for result of collector's work
        dupeFilter - counting filter for duplicate reads
        adapterFilter - counting filter for adapter reads
        mapqFilter - counting filter for mapping quality
        pairFilter - counting filter for reads without a mapped mate pair
      • getDepthHistogram

        protected htsjdk.samtools.util.Histogram<Integer> getDepthHistogram()
      • areHistogramsEmpty

        public boolean areHistogramsEmpty()